Sorting by Short Block-Moves |
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Authors: | L. S. Heath J. P. C. Vergara |
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Affiliation: | (1) Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0106, USA. heath@cs.vt.edu., US;(2) Department of Information Systems and Computer Science, Ateneo De Manila University, Manila 0917, Philippines. jpv@admu.edu.ph., PH |
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Abstract: | Sorting permutations by operations such as reversals and block-moves has received much interest because of its applications in the study of genome rearrangements and in the design of interconnection networks. A short block-move is an operation on a permutation that moves an element at most two positions away from its original position. This paper investigates the problem of finding a minimum-length sorting sequence of short block-moves for a given permutation. A 4/3 -approximation algorithm for this problem is presented. Woven double-strip permutations are defined and a polynomial-time algorithm for this class of permutations is devised that employs graph matching techniques. A linear-time maximum matching algorithm for a special class of grid graphs improves the time complexity of the algorithm for woven double-strip permutations. Received June 1, 1997; revised July 25, 1998. |
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Keywords: | . Computational biology Genome rearrangement Approximation algorithms Maximum matching Permutations. |
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